Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Hnf4a

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
Liver
Sex
male
genotype
exon swap a7HMZ (P2-HNF4a only)
age
16 to 20 weeks
diet
fed ad libitum (LabDiet, #5001)
strain
mixed 129/Sv plus C57BL/6 background
cell type
Liver
chip antibody
HNF4a (alpha-445)
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM7290595
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fresh tissue was fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a Sonic Dismembtrator 500 (Fisher Scientific). DNA fragments with 200-500 bps were selected ChIP-seq libraries were prepared using the BIOO Scientific ChIPseq DNA library kit. 2-22 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using a thermocycler. Libraries were validated using ???

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
28568911
Reads aligned (%)
98.3
Duplicates removed (%)
21.8
Number of peaks
58639 (qval < 1E-05)

mm9

Number of total reads
28568911
Reads aligned (%)
98.2
Duplicates removed (%)
21.9
Number of peaks
58669 (qval < 1E-05)

Base call quality data from DBCLS SRA